Energy, Enzymes, and Biological Reactions

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Energy, Enzymes, and Biological Reactions

• Chapter 4

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Energy

• Definition The Capacity to do work
• Types of Energy
• Potential Stored energy, measured as a capacity
  to do work. example stretched spring
• Kinetic Energy of motion, released potential
  energy. example releasing of a stretched spring
• Thermal Energy released as heat
• Chemical Potential energy stored in molecules.
  Measured as Kilocalories (Kcal) aka Calories (C)
• (1 calorie (c) heat reqd to raise 1g of H2O
  1?C)

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Why do cells need energy?

• Chemical work, build, rearrange, tear apart
  compounds
• Mechanical work, move cilia, flex a muscle
• Electrochemical work, nerve impulses

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Where does energy come from?

• The universe contains a huge, but finite amount
  of energy
• The original source of energy for most life on
  earth is from the sun
• Energy is governed by the Laws of Thermodynamics

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First Law of Thermodynamics

• The total amount of energy in the universe
  remains constant
• Energy can be converted from one form to another,
  but it is never destroyed

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Second Law of Thermodynamics

• Entropy tends to increase in a closed system
• (No energy conversion is 100 efficient)
• Overall energy flows in one direction from
  useable (lots of potential energy) to nonuseable
  (little potential energy) forms

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So how can life exist?

• Energy flows from the sun to plants, which lose
  energy directly or indirectly to other organisms
• Overall energy flows in one direction and entropy
  increases as at each step energy is lost
• Producers builds complex molecules from simpler
  building blocks using the energy of the sun
• i.e. the sun is constantly supplying us with
  new energy

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Energy and chemical reactions

• Reactant(s) ? Product(s)
• Energy is stored in chemical bonds all
  molecules contain energy
• Endergonic reactions reactions in which the
  products contain more energy than reactants
• Exergonic reactions reactions in which the
  products contain less energy than the reactants

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Endergonic Reactions

• Requires energy input

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Endergonic Reaction Photosynthesis

• Original source of energy for most life on earth
• Overall reaction
• 6CO2 6H2O ? C6H12O6 6O2
• Very endergonic where does the plant get the
  energy?
• ? SUN

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Exergonic Reactions

• Releases energy

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Exergonic Reaction Cellular Respiration

• Breakdown of glucose very exergonic
• The source of ATP energy in cells
• Overall reaction
• C6H12O6 6O2 ? 6CO2 6H2O -686Kcal

glucose - energy-rich starting substance
6O2
Energy out
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products with less energy
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Adenosine Triphosphate (ATP)

• ATP is the cells energy currency nearly all
  energy in a cell is stored within the ATP
  molecule
• Energy releasing rxns? ATP? Energy requiring rxns
• Cells cleave ATP into ADP Pi releasing energy
• This energy can be used to do work such as
  synthesize other molecules or move muscles

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How is ATP synthesized?

• ATP are renewable and are recycled by cells

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How is the energy from ATP utilized?

• Reaction coupling thermodynamically unfavorable
  reactions (endergonic) are coupled to the
  favorable reactions of ATP cleavage (exergonic)
• ATP ? ADP Pi 7.3Kcal
• X ? ? ? ? Y 5Kcal
• Net energy -2.3Kcal
• Total reaction still increases entropy and
  conforms to the 2nd Law of Thermodynamics

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Chemical Reactions (Rxn)

• The conversion, accumulation, disposal of
  substances by a cell is done through
  energy-driven reactions
• Parts of a Reaction (Rxn)
• Reactants substances that enter into a reaction
• Intermediates substances formed in the middle of
  a reaction
• Products end results of a reaction

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How are cellular reactions defined?
 

• Catabolism breaking down of complex molecules
• Anabolism the building up of complex molecules
• Metabolism the sum of all these reactions

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Anabolic and Catabolic Reactions
large energy-rich molecules
ADP Pi
BIOSYNTHETIC PATHWAYS (ANABOLIC)
DEGRADATIVE PATHWAYS (CATABOLIC)
ATP
simple organic compounds
energy-poor products
ENERGY INPUT
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Types of Reaction Sequences
A
B
C
D
E
F
LINEAR PATHWAY
CYCLIC PATHWAY
G
K
J
I
BRANCHING PATHWAY
N
M
L
H
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Activation Energy

• Exergonic reactions are spontaneous - Why dont
  exergonic reactions happen all the time?
• Because of Activation Energy (EA) the energy
  required to get a reaction started
• The EA of a reaction can prevent it from
  occurring or cause it to occur slowly

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Activation Energy

• Initial input of energy to start a reaction, even
  if it is spontaneous

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Catalysts

• Agents that speed up chemical reactions without
  getting used up

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Biological Catalysts Enzymes

• Enzymes are protein catalysts (ribozymes are RNA
  catalysts)
• They are required in small amounts
• They are not altered permanently by the reaction
• They do not change the thermodynamics of a
  reaction
• They can only accelerate the rate at which a
  favorable reaction proceeds

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Role of Enzymes in Biological Reactions

• Enzymes accelerate reactions by reducing
  activation energy
• Enzymes combine with reactants and are released
  unchanged
• Enzymes reduce activation energy by inducing the
  transition state

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Enzymes and Activation Energy

• Enzymes decrease activation energy required for a
  chemical reaction to proceed

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Biological Catalysts
Example A phosphatase enzyme can catalyze a rxn
in 10 milliseconds Without the enzyme the rxn
would take 1 trillion yrs. (1,000,000,000,000) TH
E REACTION IS CONSIDERED SPONTANEOUS
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Enzyme Specificity

• Enzymes are usually very specific
• Substrates interact with enzymes active site

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Enzyme ActivityInduced Fit Model
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Transition State

• During catalysis, the substrate and active site
  form an intermediate transition state

Fig. 4-12, p. 81
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How do enzymes lower EA?

• Catalytic mechanisms induce transition state
• Bringing substrates into close proximity
• Orienting substrates
• Altering environment around substrates

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Factors That Affect Enzymes

• Temperature
• increasing temperature speeds up rxns (both
  enzymatic and non-enzymatic) up to a point (WHY?)
• High temperatures will destroy the enzyme
• Enzymes are proteins
• Proteins get denatured (unfolded) at high temps

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Factors That Affect Enzymes

• Concentration of substrate and products
• increasing substrate will increase reaction up to
  a point
• increased product will slow reaction (known as
  negative feedback)
• Concentration of enzyme
• Increasing concentration increases enzyme
  activity up to a point

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Factors That Affect Enzymes

• pH
• H affects enzyme shape, so enzymes work best
  at narrow ranges of pH
• Optimal pH pH at which enzyme can catalyze best
• For most enzymes, optimal pH is around neutral,
  depending on the environment in which the enzymes
  work
• E.g. Pepsin digestive enzyme in stomach,
  optimal pH 2

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Controlling Enzyme Activity

• Enzymes are very efficient at what they do
• Because of this they need to be carefully
  controlled
• The cells needs to be able to regulate when a
  reaction occurs
• The cell also has to be able to regulate how much
  product is produced from a reaction

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Enzyme inhibitors

• Competitive inhibitors
• Bind to active site of enzyme
• Prevent substrate from binding
• Non-competitive inhibitors
• Also called Allosteric inhibitors
• Bind to enzyme in a region other than the active
  site called allosteric site
• Change the shape of the active site to prevent
  substrates from binding

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Enzyme Regulation

• Enzyme activity is often regulated to meet the
  needs for reaction products
• Allosteric regulation occurs with reversible
  combinations of regulatory molecules with an
  allosteric site on the enzyme
• High-affinity state (active form) enzyme binds
  substrate strongly
• Low-affinity state (inactive form)enzyme binds
  substrate weakly or not at all

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Allosteric Regulation

• Allosteric activators and allosteric inhibitors

Fig. 4-17, p. 84
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Feedback inhibition

• If too much product is created the first enzyme
  may be shut off by the product becoming an
  allosteric or competitive inhibitor

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Cofactors and Coenzymes

• Some enzymes need assistance in the form of
  cofactors
• Minerals inorganic cofactors
• Examples Potassium, Sodium, Calcium
• Vitamins organic cofactors or coenzymes
• Examples The specialized nucleotides NAD and
  FAD act as cofactors for enzymatic reactions
  NAD contains the vitamin niacin and FAD contains
  the vitamin riboflavin

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Ribozymes

• RNA-based catalysts
• Help remove surplus segments of RNA molecules
  with cutting and splicing reactions
• In ribosomes, help join amino acids together when
  building proteins

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Some coenzymes accept and hold onto electrons
(e-) and protons (H) during the breakdown glucose
Why are these coenzymes required? Enzymes are not
used up or modified during a reaction If the
enzyme accepted the e- or H it would be modified
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Oxidation/Reduction (Redox) Reactions One
compound gains e- or H lost by another
compound The oxidized compound loses electrons or
H The reduced compound gains electrons or
H Reduction acts as a mechanism for storing
energy
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Redox Reactions